Methylotrophy in a lake: from metagenomics to single-organism physiology

Unveiling complete natural reductive dechlorination mechanisms of chlorinated ethenes in groundwater: Insights from functional gene analysis

Monitored natural attenuation (MNA) of chlorinated ethenes (CEs) has proven to be a cost-effective and environment-friendly approach for groundwater remediation. In this study, the complete dechlorination of CEs with formation of ethene under natural conditions, were observed at two CE-contaminated sites, including a pesticide manufacturing facility (PMF) and a fluorochemical plant (FCP), particularly in the deeply weathered bedrock aquifer at the FCP site. Additionally, a higher abundance of CE-degrading bacteria was identified with heightened dechlorination activities at the PMF site, compared to the FCP site. The reductive dehalogenase genes and Dhc 16 S rRNA gene were prevalent at both sites, even in groundwater where no CE dechlorination was observed. vcrA and bvcA was responsible for the complete dechlorination at the PMF and FCP site, respectively, indicating the distinct contributions of functional microbial species at each site. The correlation analyses suggested that Sediminibacterium has the potential to achieve the complete dechlorination at the FCP site. Moreover, the profiles of CE-degrading bacteria suggested that dechlorination occurred under Fe3+/sulfate-reducing and nitrate-reducing conditions at the PMF and FCP site, respectively. Overall these findings provided multi-lines of evidence on the diverse mechanisms of CE-dechlorination under natural conditions, which can provide valuable guidance for MNA strategies implementation.

The Proteobacterial Methanotroph Methylosinus trichosporium OB3b Remodels Membrane Lipids in Response to Phosphate Limitation

Methane is a potent greenhouse gas in the atmosphere, and its concentration has continued to increase in recent decades. Aerobic methanotrophs, bacteria that use methane as the sole carbon source, are an important biological sink for methane, and they are widely distributed in the natural environment. However, relatively little is known on how methanotroph activity is regulated by nutrients, particularly phosphorus (P). P is the principal nutrient constraining plant and microbial productivity in many ecosystems, ranging from agricultural land to the open ocean. Using a model methanotrophic bacterium, Methylosinus trichosporium OB3b, we demonstrate here that this bacterium can produce P-free glycolipids to replace membrane phospholipids in response to P limitation. The formation of the glycolipid monoglucuronic acid diacylglycerol requires plcP-agt genes since the plcP-agt mutant is unable to produce this glycolipid. This plcP-agt-mediated lipid remodeling pathway appears to be important for M. trichosporium OB3b to cope with P stress, and the mutant grew significantly slower under P limitation. Interestingly, comparative genomics analysis shows that the ability to perform lipid remodeling appears to be a conserved trait in proteobacterial methanotrophs; indeed, plcP is found in all proteobacterial methanotroph genomes, and plcP transcripts from methanotrophs are readily detectable in metatranscriptomics data sets. Together, our study provides new insights into the adaptation to P limitation in this ecologically important group of bacteria.

RNA stable isotope probing and high-throughput sequencing to identify active microbial community members in a methane-driven denitrifying biofilm

AIMS

Aerobic methane oxidation coupled to denitrification (AME-D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA-SIP) and high-throughput sequencing to identify the micro-organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm.

METHODS AND RESULTS

Two RNA-SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to ¹³ C-labelled methane over a 96-hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of ¹³ C labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed ¹³ C enrichment of the RNA. The RNA-SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high-throughput sequencing identified the active micro-organisms enriched with ¹³ C.

CONCLUSIONS

Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME-D.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to use RNA-SIP and high-throughput sequencing to determine the bacteria active within an AME-D community.

Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities

The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β- and γ-carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified, although absence of key genes and failure to identify a photosynthetic reaction center preclude proposing phototrophic capacities. Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.IMPORTANCE A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. We present evidence that members of the order Binatota specialize in methylotrophy and identify an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds in Binatota genomes. The occurrence of multiple alkane hydroxylases and monooxygenases in these genomes was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. We also report on the presence of incomplete chlorophyll biosynthetic pathways in all genomes and propose several evolutionary-grounded scenarios that could explain such a pattern. Assessment of the ecological distribution patterns of the Binatota indicates preference of its members to terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.

Analysis of Different Size Fractions Provides a More Complete Perspective of Viral Diversity in a Freshwater Embayment

Inspired by recent discoveries of the prevalence of large viruses in the environment, we reassessed the longstanding approach of filtering water through small-pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 data sets derived from <0.45-μm- and >0.45-μm-size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family, we observed highly diverse and distinct virus communities in the >0.45-μm-size fractions, whereas the <0.45-μm-size fractions were composed primarily of Caudovirales The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions, with higher relative abundances of cyanophages in the >0.45-μm-size fractions, potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, were detected exclusively in the often-disregarded >0.45-μm-size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions, suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of double-stranded DNA (dsDNA) viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing.IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller-size "free-virus" fraction. Our study demonstrates that analysis of virus communities using only the smaller-size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger->0.45-μm-size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data show that examining only the smaller-size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.

Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake

In stratified lakes, methane-oxidizing bacteria (MOB) are strongly mitigating methane fluxes to the atmosphere by consuming methane entering the water column from the sediments. MOB communities in lakes are diverse and vertically structured, but their spatio-temporal dynamics along the water column as well as physico-chemical parameters and interactions with other bacterial species that drive the community assembly have so far not been explored in depth. Here, we present a detailed investigation of the MOB and bacterial community composition and a large set of physico-chemical parameters in a shallow, seasonally stratified, and sub-alpine lake. Four highly resolved vertical profiles were sampled in three different years and during various stages of development of the stratified water column. Non-randomly assembled MOB communities were detected in all compartments. We could identify methane and oxygen gradients and physico-chemical parameters like pH, light, available copper and iron, and total dissolved nitrogen as important drivers of the MOB community structure. In addition, MOB were well-integrated into a bacterial-environmental network. Partial redundancy analysis of the relevance network of physico-chemical variables and bacteria explained up to 84% of the MOB abundances. Spatio-temporal MOB community changes were 51% congruent with shifts in the total bacterial community and 22% of variance in MOB abundances could be explained exclusively by the bacterial community composition. Our results show that microbial interactions may play an important role in structuring the MOB community along the depth gradient of stratified lakes.

Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function

The lanthanide elements (Ln³⁺), those with atomic numbers 57-63 (excluding promethium, Pm³⁺), form a cofactor complex with pyrroloquinoline quinone (PQQ) in bacterial XoxF methanol dehydrogenases (MDHs) and ExaF ethanol dehydrogenases (EDHs), expanding the range of biological elements and opening novel areas of metabolism and ecology. Other MDHs, known as MxaFIs, are related in sequence and structure to these proteins, yet they instead possess a Ca²⁺-PQQ cofactor. An important missing piece of the Ln³⁺ puzzle is defining what features distinguish enzymes that use Ln³⁺-PQQ cofactors from those that do not. Here, using XoxF1 MDH from the model methylotrophic bacterium Methylorubrum extorquens AM1, we investigated the functional importance of a proposed lanthanide-coordinating aspartate residue. We report two crystal structures of XoxF1, one with and another without PQQ, both with La³⁺ bound in the active-site region and coordinated by Asp³²⁰ Using constructs to produce either recombinant XoxF1 or its D320A variant, we show that Asp³²⁰ is needed for in vivo catalytic function, in vitro activity, and La³⁺ coordination. XoxF1 and XoxF1 D320A, when produced in the absence of La³⁺, coordinated Ca²⁺ but exhibited little or no catalytic activity. We also generated the parallel substitution in ExaF to produce ExaF D319S and found that this variant loses the capacity for efficient ethanol oxidation with La³⁺ These results provide evidence that a Ln³⁺-coordinating aspartate is essential for the enzymatic functions of XoxF MDHs and ExaF EDHs, supporting the notion that sequences of these enzymes, and the genes that encode them, are markers for Ln³⁺ metabolism.

New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics

Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.

Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae

The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters ("Ca. Methylopumilus") and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal

We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.

Synthetic Methane-Consuming Communities from a Natural Lake Sediment

The metabolism of methane is an important part of the global carbon cycle. While deciphering the community function and the potential role of the different functional guilds is very difficult when considering native complex communities, synthetic communities, built of species originating from a study site in question, present a simplified model and allow specific questions to be addressed as to carbon, nitrogen, and other nutrient transfer among species in a controlled system. This study applies an ecophysiological approach, as a proof of principle, to an already well-studied model system, contributing to a better understanding of microbial community function and microbial ecosystem processes.

The factors and processes that influence the behavior and functionality of ecosystems inhabited by complex microbiomes are still far from being clearly understood. Synthetic microbial communities provide reduced-complexity models that allow an examination of ecological theories under defined and controlled conditions. In this study, we applied a multiphasic approach to study synthetic methane-oxidizing communities and species interactions as proxies to the natural communities. Our results confirm that, under selective pressures, natural-sediment communities of high complexity simplify rapidly, selecting for several major functional guilds, the major partners in methane oxidation being the Methylococcaceae methanotrophs and the Methylophilaceae methylotrophs, along with minor but persistent partners, members of Burkholderiales and Flavobacteriales. As a proof of concept, we established minimalist synthetic communities that were representative of the four functional guilds to demonstrate the dependency of the non-methane-utilizing species on the methanotrophs as the primary carbon-providing species. We observed that in communities consisting of multiple representatives of the key guilds, members of the same guild appeared to compete for resources. For example, when two methanotrophs of the same family were present, the two expressed similar key methanotrophy pathways and responded similarly to changing environmental conditions, suggesting that they perform a similar keystone function in situ. Similar observations were made for the Methylophilaceae. However, differences were noted in the expression of auxiliary and unique genes among strains of the same functional guild, reflecting differential adaptation and suggesting mechanisms for competition. At the same time, differences were also noted in the performances of partners with specific metabolic schemes. For example, a mutant of Methylotenera mobilis impaired in nitrate utilization behaved as a more efficient cooperator in methane consumption, suggesting that the loss of function may lead to changes in communal behavior. Overall, we demonstrate the robust nature of synthetic communities built of native lake sediment strains and their utility in addressing important ecological questions while using a simplified model.

Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment

Bacterial community structure and metabolism are critical factors for ecosystem functioning since they affect remineralization of nutrients and carbon flow. We used Illumina sequencing of 16SrRNA V3-V4 regions to investigate whether bacterial assemblage composition differs between four samples from two lakes in the geographic region of Epirus (Greece) characterized by distinct oligotrophic to eutrophic/hypereutrophic conditions as revealed by chlorophyll-a values. We found high similarity (>60%) for bacterial assemblages recovered from the two lakes when eutrophic/hypereutrophic conditions prevailed. Distinct bacterial communities appeared in oligotrophic and mesotrophic waters. Low temperature was occasionally an important factor in shaping the bacterial community. In parallel, microcosm experiments were performed to estimate respiration rates of bacterioplankton at in situ temperature and under a 2 °C temperature increase scenario. Differently assembled communities were found to display similar rates except under hypereutrophic conditions when respiration increased significantly, leading to hypoxic conditions. Temperature increase did not affect respiration rates. Overall this study indicated a clear differentiation of bacterial communities between sites of different trophic state. However, different communities responded similarly under a specific range of chlorophyll-a values and resisted small scale temperature perturbations. Different results were found for hypereutrophic conditions and this has implications for ecosystems functioning, given the increasing occurrence of eutrophication events.

Methylococcaceae are the dominant active aerobic methanotrophs in a Chinese tidal marsh

Although coastal marshes are net carbon sinks, they are net methane sources. Aerobic methanotrophs in coastal marsh soils are important methane consumers, but their activity and populations are poorly characterized. DNA stable-isotope probing followed by sequencing was used to determine how active methanotrophic populations differed in the main habitats of a Chinese coastal marsh. These habitats included mudflat, native plant-dominated, and alien plant-dominated habitats. Methylococcaceae was the most active methanotroph family across four habitats. Abundant methylotroph sequences, including methanotrophs and non-methane-oxidizing methylotrophs (Methylotenera and Methylophaga), constituted 50-70% of the 16S rRNA genes detected in the labeled native plant-dominated and mudflat soils. Methylotrophs were less abundant (~ 20%) in labeled alien plant-dominated soil, suggesting less methane assimilation into the target community or a different extent of carbon cross-feeding. Canonical correspondence analysis indicated a significant correlation between the active bacterial communities and soil properties (salinity, organic carbon, total nitrogen, pH, and available phosphorus). Importantly, these results highlight how changing vegetation or soil features in coastal marshes may change their resident active methanotrophic populations, which will further influence methane cycling.

Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland

Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie. 16S rRNA gene analyses demonstrated that members of the methanotrophic Methylococcales were dominant, with the dominance largely driven by the relative abundance of four taxa, and enriched in oxic surface soils. Three methanotroph genomes from assembled soil metagenomes were assigned to the genus Methylobacter and represented the most abundant methanotrophs across the wetland. Paired metatranscriptomes confirmed that these Old Woman Creek (OWC) Methylobacter members accounted for nearly all the aerobic methanotrophic activity across two seasons. In addition to having the capacity to couple methane oxidation to aerobic respiration, these new genomes encoded denitrification potential that may sustain energy generation in soils with lower dissolved oxygen concentrations. We further show that Methylobacter members that were closely related to the OWC members were present in many other high-methane-emitting freshwater and soil sites, suggesting that this lineage could participate in methane consumption in analogous ecosystems. This work contributes to the growing body of research suggesting that Methylobacter may represent critical mediators of methane fluxes in freshwater saturated sediments and soils worldwide.IMPORTANCE Here we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter We denote these closely related genomes as members of the lineage OWC Methylobacter Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production ("Candidatus Methanothrix paradoxum") and methane consumption (OWC Methylobacter). Metatranscriptomic analyses revealed that decreased methanotrophic activity rather than increased methanogenic activity possibly contributed to the greater methane emissions that we had previously observed in summer months, findings important for biogeochemical methane models. Although members of this Methylococcales order have been cultivated for decades, multi-omic approaches continue to illuminate the methanotroph phylogenetic and metabolic diversity harbored in terrestrial and marine ecosystems.

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)

Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.

Pyrroloquinoline Quinone Ethanol Dehydrogenase in Methylobacterium extorquens AM1 Extends Lanthanide-Dependent Metabolism to Multicarbon Substrates

Lanthanides are utilized by microbial methanol dehydrogenases, and it has been proposed that lanthanides may be important for other type I alcohol dehydrogenases. A triple mutant strain (mxaF xoxF1 xoxF2; named MDH-3), deficient in the three known methanol dehydrogenases of the model methylotroph Methylobacterium extorquens AM1, is able to grow poorly with methanol if exogenous lanthanides are added to the growth medium. When the gene encoding a putative quinoprotein ethanol dehydrogenase, exaF, was mutated in the MDH-3 background, the quadruple mutant strain could no longer grow on methanol in minimal medium with added lanthanum (La³⁺). ExaF was purified from cells grown with both calcium (Ca²⁺) and La³⁺ and with Ca²⁺ only, and the protein species were studied biochemically. Purified ExaF is a 126-kDa homodimer that preferentially binds La³⁺ over Ca²⁺ in the active site. UV-visible spectroscopy indicates the presence of pyrroloquinoline quinone (PQQ) as a cofactor. ExaF purified from the Ca²⁺-plus-La³⁺ condition readily oxidizes ethanol and has secondary activities with formaldehyde, acetaldehyde, and methanol, whereas ExaF purified from the Ca²⁺-only condition has minimal activity with ethanol as the substrate and activity with methanol is not detectable. The exaF mutant is not affected for growth with ethanol; however, kinetic and in vivo data show that ExaF contributes to ethanol metabolism when La³⁺ is present, expanding the role of lanthanides to multicarbon metabolism.

IMPORTANCE

ExaF is the most efficient PQQ-dependent ethanol dehydrogenase reported to date and, to our knowledge, the first non-XoxF-type alcohol oxidation system reported to use lanthanides as a cofactor, expanding the importance of lanthanides in biochemistry and bacterial metabolism beyond methanol dehydrogenases to multicarbon metabolism. These results support an earlier proposal that an aspartate residue near the catalytic aspartate residue may be an indicator of rare-earth element utilization by type I alcohol dehydrogenases.

Methylotrophs in natural habitats: current insights through metagenomics

The focus of this review is on the recent data from the omics approaches, measuring the presence of methylotrophs in natural environments. Both Bacteria and Archaea are considered. The data are discussed in the context of the current knowledge on the biochemistry of methylotrophy and the physiology of cultivated methylotrophs. One major issue discussed is the recent metagenomic data pointing toward the activity of "aerobic" methanotrophs, such as Methylobacter, in microoxic or hypoxic conditions. A related issue of the metabolic distinction between aerobic and "anaerobic" methylotrophy is addressed in the light of the genomic and metagenomic data for respective organisms. The role of communities, as opposed to single-organism activities in environmental cycling of single-carbon compounds, such as methane, is also discussed. In addition, the emerging issue of the role of non-traditional methylotrophs in global metabolism of single-carbon compounds and the role of methylotrophy pathways in non-methylotrophs is briefly mentioned.

SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment

Dimethylsulphide (DMS) has an important role in the global sulphur cycle and atmospheric chemistry. Microorganisms using DMS as sole carbon, sulphur or energy source, contribute to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, a wide range of bacteria isolated from terrestrial ecosystems were shown to be able to degrade DMS, yet it remains unknown whether any of these have important roles in situ. In this study, we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by denaturing gradient gel electrophoresis, high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA. Labelling patterns of time course SIP experiments identified members of the Methylophilaceae family, not previously implicated in DMS degradation, as dominant DMS-degrading populations in soil and lake sediment. Thiobacillus spp. were also detected in ¹³C-DNA from SIP incubations. Metagenomic sequencing also suggested involvement of Methylophilaceae in DMS degradation and further indicated shifts in the functional profile of the DMS-assimilating communities in line with methylotrophy and oxidation of inorganic sulphur compounds. Overall, these data suggest that unlike in the marine environment where gammaproteobacterial populations were identified by SIP as DMS degraders, betaproteobacterial Methylophilaceae may have a key role in DMS cycling in terrestrial environments.

Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway

Methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single carbon compounds, methylotrophs, serve as a major biological sink for methylamine in aerobic environments. Two non-orthologous, functionally degenerate routes for methylamine oxidation have been studied in methylotrophic Proteobacteria: Methylamine dehydrogenase and the N-methylglutamate pathway. Recent work suggests the N-methylglutamate (NMG) pathway may be more common in nature than the well-studied methylamine dehydrogenase (MaDH, encoded by the mau gene cluster). However, the distribution of these pathways across methylotrophs has never been analyzed. Furthermore, even though horizontal gene transfer (HGT) is commonly invoked as a means to transfer these pathways between strains, the physiological barriers to doing so have not been investigated. We found that the NMG pathway is both more abundant and more universally distributed across methylotrophic Proteobacteria compared to MaDH, which displays a patchy distribution and has clearly been transmitted by HGT even amongst very closely related strains. This trend was especially prominent in well-characterized strains of the Methylobacterium extroquens species, which also display significant phenotypic variability during methylamine growth. Strains like Methylobacterium extorquens PA1 that only encode the NMG pathway grew on methylamine at least five-fold slower than strains like Methylobacterium extorquens AM1 that also possess the mau gene cluster. By mimicking a HGT event through the introduction of the M. extorquens AM1 mau gene cluster into the PA1 genome, the resulting strain instantaneously achieved a 4.5-fold increase in growth rate on methylamine and a 11-fold increase in fitness on methylamine, which even surpassed the fitness of M. extorquens AM1. In contrast, when three replicate populations of wild type M. extorquens PA1 were evolved on methylamine as the sole carbon and energy source for 150 generations neither fitness nor growth rate improved. These results suggest that the NMG pathway permits slow growth on methylamine and is widely distributed in methylotrophs; however, rapid growth on methylamine can be achieved quite readily through acquisition of the mau cluster by HGT.

Methylamine utilization via the N-methylglutamate pathway in Methylobacterium extorquens PA1 involves a novel flow of carbon through C1 assimilation and dissimilation pathways

Methylotrophs grow on reduced single-carbon compounds like methylamine as the sole source of carbon and energy. In Methylobacterium extorquens AM1, the best-studied aerobic methylotroph, a periplasmic methylamine dehydrogenase that catalyzes the primary oxidation of methylamine to formaldehyde has been examined in great detail. However, recent metagenomic data from natural ecosystems are revealing the abundance and importance of lesser-known routes, such as the N-methylglutamate pathway, for methylamine oxidation. In this study, we used M. extorquens PA1, a strain that is closely related to M. extorquens AM1 but is lacking methylamine dehydrogenase, to dissect the genetics and physiology of the ecologically relevant N-methylglutamate pathway for methylamine oxidation. Phenotypic analyses of mutants with null mutations in genes encoding enzymes of the N-methylglutamate pathway suggested that γ-glutamylmethylamide synthetase is essential for growth on methylamine as a carbon source but not as a nitrogen source. Furthermore, analysis of M. extorquens PA1 mutants with defects in methylotrophy-specific dissimilatory and assimilatory modules suggested that methylamine use via the N-methylglutamate pathway requires the tetrahydromethanopterin (H4MPT)-dependent formaldehyde oxidation pathway but not a complete tetrahydrofolate (H4F)-dependent formate assimilation pathway. Additionally, we present genetic evidence that formaldehyde-activating enzyme (FAE) homologs might be involved in methylotrophy. Null mutants of FAE and homologs revealed that FAE and FAE2 influence the growth rate and FAE3 influences the yield during the growth of M. extorquens PA1 on methylamine.

Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response

We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples. We first measured taxonomic compositions of long-term enrichment cultures and determined that, although dominated by Methylococcaceae types, these cultures also contained accompanying types belonging to a limited number of bacterial taxa, methylotrophs and non-methylotrophs. We then followed the short-term community dynamics, in two oxygen tension regimens (150 μM and 15 μM), observing rapid loss of species diversity. In all microcosms, a single type of Methylobacter represented the major methane-oxidizing partner. The accompanying members of the communities revealed different trajectories in response to different oxygen tensions, with Methylotenera species being the early responders to methane stimulus under both conditions. The communities in both conditions were convergent in terms of their assemblage, suggesting selection for specific taxa. Our results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are likely responsible for methane cycling, rather than a single type of microbe.

The expanded diversity of methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes

We describe five novel Methylophilaceae ecotypes from a single ecological niche in Lake Washington, USA, and compare them to three previously described ecotypes, in terms of their phenotype and genome sequence divergence. Two of the ecotypes appear to represent novel genera within the Methylophilaceae. Genome-based metabolic reconstruction highlights metabolic versatility of Methylophilaceae with respect to methylotrophy and nitrogen metabolism, different ecotypes possessing different combinations of primary substrate oxidation systems (MxaFI-type methanol dehydrogenase versus XoxF-type methanol dehydrogenase; methylamine dehydrogenase versus N-methylglutamate pathway) and different potentials for denitrification (assimilatory versus respiratory nitrate reduction). By comparing pairs of closely related genomes, we uncover that site-specific recombination is the main means of genomic evolution and strain divergence, including lateral transfers of genes from both closely- and distantly related taxa. The new ecotypes and the new genomes contribute significantly to our understanding of the extent of genomic and metabolic diversity among organisms of the same family inhabiting the same ecological niche. These organisms also provide novel experimental models for studying the complexity and the function of the microbial communities active in methylotrophy.

Is metagenomics resolving identification of functions in microbial communities?

We are coming up on the tenth anniversary of the broad use of the method involving whole metagenome shotgun sequencing, referred to as metagenomics. The application of this approach has definitely revolutionized microbiology and the related fields, including the realization of the importance of the human microbiome. As such, metagenomics has already provided a novel outlook on the complexity and dynamics of microbial communities that are an important part of the biosphere of the planet. Accumulation of massive amounts of sequence data also caused a surge in the development of bioinformatics tools specially designed to provide pipelines for data analysis and visualization. However, a critical outlook into the field is required to appreciate what could be and what has currently been gained from the massive sequence databases that are being generated with ever-increasing speed.

Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation

We carried out whole transcriptome analysis of three species of Methylophilaceae, Methylotenera mobilis, Methylotenera versatilis and Methylovorus glucosotrophus, in order to determine which metabolic pathways are actively transcribed in cultures grown in laboratory on C1 substrates and how metabolism changes under semi-in situ conditions. Comparative analyses of the transcriptomes were used to probe the metabolic strategies utilized by each of the organisms in the environment. Our analysis of transcript abundance data focused on changes in expression of methylotrophy metabolic modules, as well as on identifying any functional modules with pronounced response to in situ conditions compared to a limited set of laboratory conditions, highlighting their potential role in environmental adaptation. We demonstrate that transcriptional responses to environmental conditions involved both methylotrophy and non-methylotrophy metabolic modules as well as modules responsible for functions not directly connected to central metabolism. Our results further highlight the importance of XoxF enzymes that were previously demonstrated to be highly expressed in situ and proposed to be involved in metabolism of methanol by Methylophilaceae. At the same time, it appears that different species employ different homologous Xox systems as major metabolic modules. This study also reinforces prior observations of the apparent importance of the methylcitric acid cycle in the Methylotenera species and its role in environmental adaptation. High transcription from the respective gene clusters and pronounced response to in situ conditions, along with the reverse expression pattern for the ribulose monophosphate pathway that is the major pathway for carbon assimilation in laboratory conditions suggest that a switch in central metabolism of Methylotenera takes place in response to in situ conditions. The nature of the metabolite(s) processed via this pathway still remains unknown. Of the functions not related to central metabolism, flagellum and fimbria synthesis functions appeared to be of significance for environmental adaptation, based on their high abundance and differential expression. Our data demonstrate that, besides shared strategies, the organisms employed in this study also utilize strategies unique to each species, suggesting that the genomic divergence plays a role in environmental adaptation.

Insights into denitrification in Methylotenera mobilis from denitrification pathway and methanol metabolism mutants

We investigated phenotypes of mutants of Methylotenera mobilis JLW8 with lesions in genes predicted to encode functions of the denitrification pathway, as well as mutants with mutations in methanol dehydrogenase-like structural genes xoxF1 and xoxF2, in order to obtain insights into denitrification and methanol metabolism by this bacterium. By monitoring the accumulation of nitrous oxide, we demonstrate that a periplasmic nitrate reductase, NAD(P)-linked and copper-containing nitrite reductases, and a nitric oxide reductase are involved in the denitrification pathway and that the pathway must be operational in aerobic conditions. However, only the assimilatory branch of the denitrification pathway was essential for growth on methanol in nitrate-supplemented medium. Mutants with mutations in each of the two xoxF genes maintained their ability to grow on methanol, but not the double XoxF mutant, suggesting that XoxF proteins act as methanol dehydrogenase enzymes in M. mobilis JLW8. Reduced levels of nitrous oxide accumulated by the XoxF mutants compared to the wild type suggest that these enzymes must be capable of donating electrons for denitrification.

A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae

We investigated microbial communities active in methane oxidation in lake sediment at different oxygen tensions and their response to the addition of nitrate, via stable isotope probing combined with deep metagenomic sequencing. Communities from a total of four manipulated microcosms were analyzed, supplied with ¹³C-methane in, respectively, ambient air, ambient air with the addition of nitrate, nitrogen atmosphere and nitrogen atmosphere with the addition of nitrate, and these were compared to the community from an unamended sediment sample. We found that the major group involved in methane oxidation in both aerobic and microaerobic conditions were members of the family Methylococcaceae, dominated by species of the genus Methylobacter, and these were stimulated by nitrate in aerobic but not microaerobic conditions. In aerobic conditions, we also noted a pronounced response to both methane and nitrate by members of the family Methylophilaceae that are non-methane-oxidizing methylotrophs, and predominantly by the members of the genus Methylotenera. The relevant abundances of the Methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown.

Metagenomics: microbial diversity through a scratched lens

Since nucleic acids were first extracted directly from the environment and sequenced, metagenomics has grown to one of the most data-rich and pervasive techniques for understanding the taxonomic and functional diversity of microbial communities. In the last decade, cheaper sequencing has democratized the application of metagenomics and generated billions of reads, revealing staggering microbial diversity and functional complexity. However, cheaper sequencing has come at the cost of reduced sequence length, resulting in poor gene annotation and overestimates of bacterial richness and abundance. Recent improvements in sequencing technology are beginning to provide reads of sufficient length for accurate annotation and assembly of whole operons and beyond, that will once again enable experimental testing of gene function and re-capture the early successes of metagenomic investigations.